Downy mildew caused by the obligate parasite Hyaloperonospora brassicae is a devastating disease for Brassica species. Infection of Hyaloperonospora brassicae often leads to yellow spots on leaves, which significantly impacts quality and yield of pakchoi. In the present study, we conducted a comparative transcriptome between the resistant and susceptible pakchoi cultivars in response to Hyaloperonospora brassicae infection. A total of 1073 disease-resistance-related differentially expressed genes were identified using a Venn diagram. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these genes were mainly involved in plant−pathogen interaction, plant hormone signal transduction, and other photosynthesis-related metabolic processes. Analysis of the phytohormone content revealed that salicylic acid increased significantly in the resistant material after inoculation with Hyaloperonospora brassicae, whereas the contents of jasmonic acid, abscisic acid, and 1-aminocyclopropane-1-carboxylic acid decreased. Exogenous salicylic acid treatment also significantly upregulated Hyaloperonospora brassicae-induced genes, which further confirmed a crucial role of salicylic acid during pakchoi defense against Hyaloperonospora brassicae. Based on these findings, we suggest that the salicylic-acid-mediated signal transduction contributes to the resistance of pakchoi to downy mildew, and PAL1, ICS1, NPR1, PR1, PR5, WRKY70, WRKY33, CML43, CNGC9, and CDPK15 were involved in this responsive process. Our findings evidently contribute to revealing the molecular mechanism of pakchoi defense against Hyaloperonospora brassicae.

Maize, one of the world’s major food crops, is facing the challenge of rising temperature. Leaf senescence is the most significant phenotypic change of maize under heat stress at the seedling stage, but the underlying molecular mechanism is still unknown. Here, we screened for three inbred lines (PH4CV, B73, and SH19B) that showed differentially senescing phenotypes under heat stress. Among them, PH4CV showed no obviously senescing phenotype under heat stress, while SH19B demonstrated a severely senescing phenotype, with B73 being between the two extremes. Subsequently, transcriptome sequencing showed that differentially expressed genes (DEGs) were generally enriched in response to heat stress, reactive oxygen species (ROS), and photosynthesis in the three inbred lines under heat treatment. Notably, ATP synthesis and oxidative phosphorylation pathway genes were only significantly enriched in SH19B. Then, the expression differences of oxidative phosphorylation pathways, antioxidant enzymes, and senescence-related genes in response to heat stress were analyzed in the three inbred lines. In addition, we demonstrated that silencing ZmbHLH51 by virus-induced gene silencing (VIGS) inhibits the heat-stress-induced senescence of maize leaves. This study helps to further elucidate the molecular mechanisms of heat-stress-induced leaf senescence at the seedling stage of maize.

Hypocotyl length is a critical determinant for the efficiency of mechanical harvesting in pakchoi production, but the knowledge on the molecular regulation of hypocotyl growth is very limited. Here, we report a spontaneous mutant of pakchoi, lhy7.1, and identified its characteristics. We found that it has an elongated hypocotyl phenotype compared to the wild type caused by the longitudinal growth of hypocotyl cells. Different light quality treatments, transcriptome, and proteomic analyses were performed to reveal the molecular mechanisms of hypocotyl elongation. The data showed that the hypocotyl length of lhy7.1 was significantly longer than that of WT under red, blue, and white lights but there was no significant difference under dark conditions. Furthermore, we used transcriptome and label-free proteome analyses to investigate differences in gene and protein expression levels between lhy7.1 and WT. At the transcript level, 4568 differentially expressed genes (DEGs) were identified, which were mainly enriched in “plant hormone signal transduction”, “photosynthesis”, “photosynthesis–antenna proteins”, and “carbon fixation in photosynthetic organisms” pathways. At the protein level, 1007 differentially expressed proteins (DEPs) were identified and were mainly enriched in photosynthesis-related pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network of hypocotyl elongation involving plant hormone signal transduction and photosynthesis-related pathways. The findings of this study help elucidate the regulatory mechanisms of hypocotyl elongation in lhy7.1.

Whole genome doubling (WGD) triggers profound genomic and epigenetic reorganization, yet the functional dynamics of DNA methylation during this process remain incompletely resolved. Here, we integrate whole genome bisulfite sequencing (WGBS) and three-dimensional chromatin interaction data to display methylation landscapes in autotetraploid Arabidopsis thaliana. Our analysis reveals evolutionarily conserved spatial patterning of DNA methylation after WGD, with centromeric enrichment and telomeric depletion. Chromosome-level profiling identifies Chromosome 2 as the most highly methylated across CG, CHG, and CHH contexts, while Chromosome 1 shows the lowest methylation. Subcontext methylation analysis uncovers increases in methylation levels in autotetraploid Arabidopsis thaliana, most pronounced in the CHH context, yet global distribution patterns remain stable. Comparative methylation profiling around genes and transposable elements (TEs) reveals elevated CHH methylation in autotetraploid gene bodies and flanking regions, whereas TE bodies exhibit minimal changes despite minor flanking hypermethylation. Strikingly, 8% of chromatin compartments were restructured, and B-B interactions weakened in autotetraploid, while DNA methylation remained stable across shifting A/B compartments. Our findings suggest that DNA methylation serves as a resilient epigenetic modification during WGD, even if 3D chromatin architecture undergoes reorganization upon WGD in some degree.

Pakchoi is a kind of nonheading Chinese cabbage being widely cultivated not only in China but also all over Asia. High temperature is a major limiting factor influencing the yield and quality of pakchoi, while the mechanism of pakchoi dealing with high-temperature challenges remains largely elusive. In the present study, we conducted a comparative transcriptomic analysis, which was also validated by qPCR, of the heat-tolerant Xinxiaqing (XXQ) variant and Suzhouqing (SZQ) variant, which are heat-sensitive under high-temperature treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggest that high-temperature-induced phytohormones signal transduction, especially auxin signal transduction, regulates the heat responses of pakchoi. Our further investigations imply that high-temperature-activated auxin signal plays a positive role in helping pakchoi deal with high-temperature challenge; IAA-pretreated pakchoi plants exhibited greater resistance to the high-temperature treatment, probably due to the induction of antioxidant activity. In addition, our study also identified six heat shock proteins/factors (HSPs/HSFs) whose up-regulation correlates with the elevated heat tolerance of pakchoi. Notably, among these high-temperature-induced heat-responsive factors, HSP20 and HSP26.5 are under the regulation of auxin signal, and this signal cascade contributes to enhancing the thermostability of pakchoi. In the present study, we identified crucial high-temperature-responsive factors and signaling pathways in pakchoi, which help in understanding the mechanism of pakchoi coping with high-temperature challenge.

Non-heading Chinese cabbage (NHCC) is an important vegetable, and its leaves are harvested for consumption. Thus, the initiation and progression of leaf senescence in NHCC directly impact its yield and quality. In multiple plant species, NAC transcription factors are known to act as critical regulators of leaf senescence. However, in NHCC, the NAC transcription factors contributing to leaf senescence regulation remain to be identified, and the mechanisms underlying dark-induced leaf senescence remain unclear. To explore the molecular mechanisms of leaf senescence in NHCC, we stored NHCC away from light and subsequently examined dark-induced transcriptional alterations via RNA sequencing. Interestingly, three NAC transcription factors, BrNAC047, BrNAC052, and BrNAC104, were found to be potently activated by darkness. Subsequently, the virus-induced gene silencing of BrNAC047, BrNAC052, and BrNAC104 demonstrated that these three NACs act as positive regulators of dark-induced leaf senescence in NHCC. Dual-luciferase assays further confirmed that BrNAC047, BrNAC052, and BrNAC104 directly activate the promoters of certain senescence-associated genes. This study uncovers the molecular signaling pathways governing dark-induced leaf senescence in NHCC, highlighting the role of three key regulators and offering valuable molecular targets for delaying leaf senescence in NHCC.